Pyrrho DBMS

Tuesday, 2 October 2018

A basic set of window functions are supported in PyrrhoDBMS. The full set of OLAP functions as defined in ISO 9075 used to be supported and can be again if there is demand: email me if you think this would be useful or if you find any issues (my direct email at UWS is in the pyrrhodb.com download).

Saturday, 11 August 2018

This version fixes a number of long-standing bugs in Pyrrho, including the following significant areas:

Exit handlers

Check constraints

Triggers

OSPStudio

Row count

The Java Connector (PyrrhoJC) is also being fixed for Java SE, and more changes are expected.
In addition, some syntax error messages have been made more helpful. Many thanks for those who have submitted performance reports - I have tried your patience by taking so long to fix them.

Please send me details of any problems you find (malcolm.crowe@uws.ac.uk).

Thursday, 19 July 2018

A previous post on this blog (More details about RESTViews) showed the range of HTTP queries that could be automatically generated by Pyrrho from a simple View definition. This post takes extends the examples, using a set of sample MySQL databases constructed for the purpose by Fritz Laux.
A number of steps are required to set up the MYSQL databases and allow remote SELECT connections to the view, so these will not detailed here. The important point is that once the remote views have been defined to a Pyrrho database, a large set of SQL queries (with filters, aggregations and joins to other local tables) are supported using automatic creation of the appropriate SQL requests to the remote MySQL databases. The local Pyrrho database is not modified during any of these tests as none of the views are materialised and no schema changes are made. The data requested (volume of data transferred from the remote databases) is minimised as shown in these blog posts. Full technical details of the mechanism are given in the Pyrrho distribution at http://pyrrhodb.com, which contains a document "The Sierra Leone example" giving more details than are given here.
In this example, the remote view is defined in Pyrrho as follows (the syntax uses an SQL extension that Pyrrho calls RESTView): [create view patientdataSL of ("hospID" char,"hospDesc" char,"patientID" int,"rCode" int,"address" char, "birthdate" date,"admission" date,"ICD10" char,"diagnosis" char,"treatments" char) as get using hospitalssl]where hospitalssl is the following small table:

hospID

hospDesc

url

'CMH'

'Choithram Memorial Hospital'

'http://root:admin@localhost:8078/sleone/patientrecordcmh'

'HS'

'Holy Spirit Hospital'

'http://root:admin@localhost:8078/sleone/patientrecordholyspirit'

'MABESSS'

'St John of God Catholic (Mabesseneh) Hospital'

'http://root:admin@localhost:8078/sleone/patientrecordmabesss'

The first column is a key to identify the remote contributor database, at the url shown.
The remote contributor databases supply views for the given credentials containing the remaining columns in the above view definition. All three databases are in a MySQL database on localhost, and of course in a real example they would be on different hosts. The HTTP listener on port 8078 is the HTTP interface restif available at GitHub - this interface needs to run on the same server as the MySQL database but has no privileges or configuration of its own. It simply accepts one or more SQL statements from and returns SQL data in Json format.
With this setup, no further programming is required to access data from the remote views, as Pyrrho generates any MySQL queries that may be required. Further local views can be defined as indicated below and the code below includesjoins aith a local table called deomgraphicSL.
Consider the following SQL statements and the corresponding SQL queries sent to the remote contributors (Pyrrho request is in black, MySQL generated query for one remote hospital in blue):

[select * from patientdataSL where "patientID" =
10015]select 'CMH' as hospID,'Choithram Memorial Hospital' as hospDesc,patientID,rCode,address,birthdate,admission,ICD10,diagnosis,treatments from patientrecordcmh where patientID=10015select count("patientID") from patientdataSLselect COUNT(patientID) as C_298 from patientrecordcmh
This request of course returns a single row from each hospital with its number of patients and Pyrrho gives the total of these counts as 30003.select count(*) from patientdatasl where icd10='N73.4'select COUNT(*) as C_323 from patientrecordcmh where ICD10='N73.4'
This time the count is 3.select "patientID" from patientdataSL where icd10='N73.4'select patientID from patientrecordcmh where ICD10='N73.4'
Three patientIDs are returned 0 from the first hospital, 2 from the second, and 1 from the third.
[select count( *) as "numPatients", "rCode", count( *)*1.0 / "totalinhabitants" as "percentageOfPopulation" from patientdataSL natural join demographicSL where "rCode" < 1010 group by "rCode","totalinhabitants" order by "percentageOfPopulation" desc]select COUNT(*) as C_275,rCode from patientrecordcmh group by rCode having rCode < 1010
This fetches 9 rows from each hospital, and results in a table of 9 rows sorted by proportionOfPopulation.

[create view patientSummary as
select "rCode",
extract(year from "admission")-extract(year from "birthdate") as "age",
extract(year from "admission") as "adyear",
icd10,
count(*) as patients
from patientDataSL
group by "rCode", "age", "adyear", icd10]select * from patientsummary where icd10='N73.4'select rCode as rCode,(YEAR(admission)-YEAR(birthdate)) as age,(YEAR(admission) as adyear,ICD10 as ICD10,COUNT(*) as C_856 from patientrecordcmh group by rCode,age,adyear,ICD10 having ICD10='N73.4'
This gives the rCode, age and admission year for the three patients mentioned above.

create view patientAnalysis as
select * from patientSummary natural join demographicSL
select * from patientanalysis where icd10='N73.4'select rCode as rCode,(YEAR(admission)-YEAR(birthdate)) as age,(YEAR(admission) as adyear,ICD10 as ICD10,COUNT(*) as C_903 from patientrecordcmh group by rCode,age,adyear,ICD10 having ICD10='N73.4'

[select "rCode", icd10, "age", patients*100.0/"under10" as percentage from patientAnalysis where ICD10='N17.1' and "age"<10]select rCode as rCode,(YEAR(admission)-YEAR(birthdate)) as age,(YEAR(admission) as adyear,ICD10 as ICD10,COUNT(*) as C_972 from patientrecordcmh group by rCode,age,adyear,ICD10 having ICD10='N73.4'These adds to the previous details some demographic information about the regions involved. The generated SQL is similar (Pyrrho currently does not pass on the condition on the calculated field age).

[select coalesce(young.icd10,older.icd10) as "icd10", youngPat, oldPat from
(select icd10, sum(patients) as youngPat from patientsummary where "age"<10 and="" icd10="">'Z87' group by icd10) young
full join
(select icd10, sum(patients) as oldPat from patientsummary where "age">50 and icd10>'Z87' group by icd10) older
on young.icd10=older.icd10 order by youngPat desc]10>select rCode as rCode,(YEAR(admission)-YEAR(birthdate)) as age,YEAR(admission) as adyear,ICD10 as ICD10,COUNT(*) as C_253 from patientrecordcmh group by rCode,age,adyear,ICD10 having ICD10>'Z87'Each half of this join retrieves 100, 97, and 70 records from the three hospitals, and groups the results into a table with 56 rows. Also the descending order is honoured. The conversions and processing are very fast.

Saturday, 2 June 2018

An introduction to RESTViews

The essential idea with RESTView
is that the Pyrrho database allows definition of views where the data is held
on remote DBMS(s): at present, the only options are Pyrrho and MySQL. The
remote DBMS is accessible via SQL statements sent over HTTP with Json
responses.

For MySQL a simple client called RestifD
(source posted on github.com/MalcolmCrowe/restif) provides this HTTP service.
The HTTP access provides the user/password combinations set up for this purpose
within MySQL by the owners of contributor databases. In the use cases
considered here, where a query Q references a RESTView V, we assume that (a)
materialising V by Extract-transform-load is undesirable for some legal reason,
and (b) we know nothing of the internal details of contributor databases. A
single remote select statement defines each RESTView: the agreement with a
contributor does not provide any complex protocols, so that for any given Q, we
want at most one query to any contributor, compatible with the permissions
granted to us by the contributor, namely grant select on the RESTView columns.

Crucially, though, for any given
Q, we want to minimise the volume D of data transferred. We can consider how
much data Q needs to compute its results, and we rewrite the query to keep D as
low as possible. Obviously many such queries (such as the obvious select * from
V) would need all of the data. At the other extreme, if Q only refers to local
data (no RESTViews) D is always zero, so that all of this analysis is specific
to the RESTView technology.

We will add a set of
query-rewriting rules to the database engine aiming to reduce D by recursive
analysis of Q and the views and tables it references. As the later sections of
this document explain, some of these rules can be very simple, such as
filtering by rows or columns of V, while others involve performing some
aggregations remotely (extreme cases such as select count(*) from V needs only
one row to be returned). In particular, we will study the interactions between
grouped aggregations and joins. The analysis will in general be recursive,
since views may be defined using aggregations and joins of other views and
local tables.

Any given Q might not be
susceptible to such a reduction, or at least we may find that none of our rules
help, so that a possible outcome of any stage in the analysis might be to
decide not to make further changes. Since this is Pyrrho, its immutable data
structures can retain previous successful stages of query rewriting, if the
next stage in the recursion is unable to make further progress.

Although in this document the
example are mostly very simple, we aim to present the analysis in such a way as
to demonstrate the applicability of the rules to more complex cases. In other
studies, such as the Sierra Leone example, queries can reference multiple
stored queries (view definitions) and functions. For now RESTViews are only
found in Pyrrho, but in principle we could have several stages where one
RESTView is defined using other RESTViews. We also bear in mind that a query Q
might involve joins of RESTViews possibly from the same remote database(s).

There are two types of RESTView
corresponding to whether the view has one single contributor or multiple remote
databases (for examples, see the text in red below). In the simple exercises in this document, V is a RESTview with one
contributor, and W has two. In the multiple-contributors case, the view
definition always includes a list of contributors (the “using table”, VU here)
making it a simple matter to manage the list of contributors.

Setting up the tests

The test cases considered in this
document are set up as follows. Everything assumes that RestifD.exe is running
(it uses port 8078 and needs no configuration), and the MySQL server is on the
local machine.

In MySQL, at a command line

create database db

use db

create table T(E integer,F nvarchar(6))

insert into T values(3,'Three'),(6,'Six'),(4,'Vier'),(6,'Sechs')

grant all privileges on T to 'root'@'%' identified by 'admin'

create database dc

use dc

create table U(E integer,F varchar(7))

insert into U values(5,'Five'),(4,'Four'),(8,'Ate')

grant all privileges on U to 'root'@'%' identified by 'admin'

In Pyrrho: We assume OSPSvr.exe
is running, with flags such as –V -E -H. Start up a command line with ospcmd
rv. Then at the SQL> prompt:

create view V of (E int,F char) as get
'http://root:admin@localhost:8078/db/t'

create table VU (d char primary key, k int, u char)

insert into VU values ('B',4,'http://root:admin@localhost:8078/db/t')

insert into VU values ('C',1,'http://root:admin@localhost:8078/dc/u')

create view W of (E int, D char, K int, F char) as get using VU

create table M (e int primary key, n char, unique(n))

insert into M values (2,'Deux'),(3,'Trois'),(4,'Quatre')

insert into M values (5,'Cinq'),(6,'Six'),(7,'Sept')

These sample tables are of course very small. But we can still use them to show how the RESTView minimises the data returned. Much larger examples inclouding the "Sierra Leone" study have demonstrated the effectiveness of the algorithms here for large data sets, views defined in terms of other views including RESTViews, aggregations, joins of views, etc.

To see the internal workings of the database engine on the following examples, start up OSPSvr.exe with the flags mentioned above. For brevity in this blog, we does not show the results of these queries.

Simple retrieval (to be avoided)

table
V

Unsurprisingly, simple queries result in the simple requests to the remote databases

For the more complex multi-database GET USING syntax we can also filter on columns of the using table (VU in this example):

Select * from w where k>2http://root:admin@localhost:8078/db select E,'B' as D,4 as K,F from t--> 2 rows

In this case, the request only goes to one of the remote databases. Note that the value of E is supplied to the remote database, in case it is referred to in the select list of the query. Such filters can of course be combined.

Aggregations

Internally, the local database engine computes SUM(C_12) from the returned rows.

select max(f) from w having e>4http://root:admin@localhost:8078/db select MAX(F) as C_33 from t where E>4--> 1 rowshttp://root:admin@localhost:8078/dc select MAX(F) as C_33 from u where E>4--> 1 rows

Again, the local engine computes max(C_33) .

select sum(e),f from w group by f http://root:admin@localhost:8078/db select SUM(E) as C_74,F from t group by F--> 2 rowshttp://root:admin@localhost:8078/dc select SUM(E) as C_74,F from u group by F--> 3 rows

Our trivial example shows no reduction in the number of rows. A larger example would show of course that the number of rows returned in determined by the number of distinct values of the grouped column f in that database.

select count(*),k/2 as k2 from w group by k2http://root:admin@localhost:8078/db select COUNT(*) as C_11,(4/2) as K2 from t--> 1 rowshttp://root:admin@localhost:8078/dc select COUNT(*) as C_11,(1/2) as K2 from u--> 1 rows

Other aggregation functions are converted to use sums and counts from the remote databases, for example:

The local database computes the request for AVG as SUM/COUNT. Common subexpressions are also optimised:

select sum(e)*sum(e),d from w group by dhttp://root:admin@localhost:8078/db select SUM(E) as C_12,'B' as D from t group by D--> 1 rowshttp://root:admin@localhost:8078/dc select SUM(E) as C_12,'C' as D from u group by D--> 1 rows

More expression rewriting

In general, subexpressions will contain other SQL functions and a mixture of local and remote columns. The following examples illustrate the number of cases that arise.

select sum(e)+char_length(max(f)) from w http://root:admin@localhost:8078/db select SUM(E) as C_12,MAX(F) as C_14 from t--> 1 rowshttp://root:admin@localhost:8078/dc select SUM(E) as C_12,MAX(F) as C_14 from u--> 1 rowsselect count(*),sum(e)+ char_length(max(f)) as x from w group by xhttp://root:admin@localhost:8078/db select COUNT(*) as C_54,SUM(E) as C_56,MAX(F) as C_58 from t group by E,F--> 2 rowshttp://root:admin@localhost:8078/dc select COUNT(*) as C_54,SUM(E) as C_56,MAX(F) as C_58 from u group by E,F--> 3 rowsselect sum(e)+k as x,k from w group by khttp://root:admin@localhost:8078/db select SUM(E) as C_12,4 as K from t group by K--> 1 rowshttp://root:admin@localhost:8078/dc select SUM(E) as C_12,1 as K from u group by K--> 1 rows

Joins

One of the steps in constructing a RESTView is to reduce the view to the columns needed for the given query. When the RESTView is used in a join, we need to ensure that columns needed for the joinCondition are added to the list of needed columns.

Select f,n from w natural join mhttp://root:admin@localhost:8078/db select F,E from t--> 2 rowshttp://root:admin@localhost:8078/dc select F,E from u--> 3 rowsIf a grouped query uses a join whose non-remote factor has key J, an aggregation operation grouped by G can be shared with the factors of the join by applying a similar aggregation grouped by GJ. In this example, the join column is the primary key of both factors. If there is no primary key defined, then all columns are needed to form the join.Select count(*) from w natural join mhttp://root:admin@localhost:8078/db select COUNT(*) as C_178,E from t group by E--> 2 rowshttp://root:admin@localhost:8078/dc select COUNT(*) as C_178,E from u group by E--> 3 rows

Friday, 11 May 2018

In 2016 I reported on an idea for Big Live Data, and included some facilities in Pyrrho to support it. The current version of Pyrrho (11 May 2018) has better support and this blog post aims to explain the details of how it works. Basically, with Big Live Data it is not sensible to copy it all to a local database, for two reasons: (a) the copy will some be out of date or will need constant updates (b) the data doesn't belong to us in the first place.

The Pyrrho database allows definition of views where the data is held
on remote DBMS(s): at present the only options are Pyrrho and MySQL. The remote
DBMS is accessible via SQL statements sent over HTTP with Json responses. For MySQL this HTTP service is implemented by a simple RestifD client (source posted on github.com/MalcolmCrowe/restif). The HTTP access provides the user/password combination set up within MySQL.

The syntax for the view definition is basically CREATE VIEW ViewDef AS GET (url|USING table)

This means there two types of RESTView
corresponding to whether there is one single contributor with a single url or multiple remote
databases supplying data for the view.

The technical details can be
found in the Pyrrho documentation (Pyrrho.pdf and SourceIntro.pdf in the
distribution, and were presented at DBKDA 2017 in Barcelona by Fritz Laux. There is a PDF version of this blog post with full details of how to set up some simple examples, entitled "The May 2018 Version of Pyrrho".

When RESTViews are used, remote data is accessed in such a way as to minimised the amount of data transferred, and avoid storing any of it in one the local machine. In some ways this is the opposite of Extract-Transform-Load. We assume an agreement with the contributor of the data that we have SELECT permission on view(s) they have defined, and credentials to enable us to access this view on the remote DBMS. There is also an understanding that we may access this view on numerous occasions but minimising the amount of data we request.

This means that on our local DBMS (Pyrrho for now) we will apply filters and aggregations to requests for the remote data. We will analyse such results locally, and join it with local data using SQL. We will often work interactively in SQL, and we will be facilitated by automatic mechanisms that transform our SQL to contain embedded requests (in SQL) that will be sent to the remote contributor. These requests will comply with the SELECT permissions we have been given on the remote view(s).

With most query optimisation mechanisms in DBMS the goal is to get the data we need into memory where processing is faster. But in the RESTView situation the aim of optimisation is to get as much aggregation and filtering as possible done on the remote system, so that as little data as possible comes to us. And of course we don't want to have the write a program every time we want something different. Ideally any query we wish to evaluate should result in at most one query being sent to each contributor.

The multiple-contributors version of RESTView assumes that all of the contributors provide data in similar format. Most probably all of them produce this data by extracting/transforming from their databases: so their base tables probably look nothing like the view they are providing. The last thing they, or we, want is to keep having to make changes to the facility they are giving us.

So we consider what opportunities we have for keeping everyone happy. There are opportunities for filtering the data vertically (fewer columns) and horizontally (fewer rows). MySQL will soon support window functions, so we can use these. We can filter and order by expressions, selecting maximum or minimum values. Aggregations over a set of contributors requires some automated support as COUNT becomes a sum of counts from the different contributors, and AVG and STDDEV_POP also need to be implemented as a combination of partial sums.

If we are joining the returned data with something, and then doing aggregations, it is natural to want to transforms these too, moving work into the RESTView. The query can be analused to find which expressions and conditions can be computed using only remote data: this allows the conditions to be applied on the remote system. Conditions can be separated into disjunctions and some applied locally, some remotely. Some aggregations can be done on the remote systems (provided we group by keys of joins we plan to make). Common subexpressions can identified and remotely computed.

In the examples I have been working on, the SQL requests to the remote DBMS all look very different from the original view definition. In my opinion this validates the entire proposal to use simple HTTP/SQL/JSon for communication with remote DBMS, rather than an API.

Friday, 9 June 2017

Previous posts in this blog have discussed the use of HTTP for direct operations with the DBMS. With Pyrrho's support for RESTViews it becomes very important to have REST interfaces to other DBMS, and there are several products such as dreamfactory and restifydb that offer this.

From today the Pyrrho distribution includes a very simple solution for MySQL, called RestIfD , and controllers to support other DBMS will probably be added over time. There is a GitHub repository for Restif at https://github.com/MalcolmCrowe/Restif .

RestIfD should be started up by an administrator on the same host as the MySQL instance, and left running. It requires no configuration, creates no files and uses very little memory. It provides a REST service on http://localhost:8803/REST/MySQL , and all requests should include an Authentication header giving the user and password for accessing MySQL.

To obtain a list of databases in Json format, use GET to http://localhost:8803/REST/MySQL . To send one or more commands to MySQL, place them in posted data to POST http://localhost:8803/REST/MySQL .

To obtain a list of tables on database db in Json format, use GET to http://localhost:8803/REST/MySQL/db .To send one or more commands for database db to MySQL, place them in posted data to POST http://localhost:8803/REST/MySQL/db .The group of commands is executed in a single transaction.

To obtain the rows of table tb on database db, in Json format, use GET to http://localhost:8803/REST/MySQL/db/tb .

To filter these results using a where condition or document w, use GET to http://localhost:8803/REST/MySQL/db/tb/w . You can delete rows from the table by using a DELETE requests to a similar url.

To update a single row in table tb on database db, send it in Json format as posted data to POST http://localhost:8803/REST/MySQL/db/tb . The row to be updated will be identified by the key fields in the supplied data.

To add a single row to table tb in database db, send it in Json format as posted data to POST http://localhost:8803/REST/MySQL/db/tb .

Saturday, 3 June 2017

The new version completes some of the changes announced in previous posts in this blog.

A: Open Source Version and Append Storage

Append storage has been a build option for some time in Pyrrho, and the new version uses it by default for the Open Source version. Unfortunately this means that databases built with the previous default version of OSPSvr (up to 5.7) cannot be used with the new default build (v.6) because they won't have the encrypted end-of-file marker.
Workarounds for users incovenienced in this way include continuing to use v5.7 for now, manually to strip the last 5 bytes from the binary file, or rebuild v6's OSPSvr without the APPEND flag. But see the next point.
v.6 OSPSvr by default doesn't support the Distributed and Partitioned features either but again these can be restored by removing the LOCAL build flag. The Pro version by default continues to use the end-of-file tamper-proof lock and distributed/partitioned features. These have been enhanced as described below.

B: Using the latest version of C#

The codebase uses the 2017 version of C# with its shortcut implicit declarations e.g. if (x is SomeClass y), and .NET's clever new Task model for some purposes, including for Push, described next.

C: Push and Pull for update notifications

Distributed and Partitioned operation up to v 5.5 was not very scalable as transaction masters and base partitions were contacted at the start of every transaction by every replica and partition to check that the local copies were up to date. Some versions since v.5.5 have contained bugs in this area. This is now remedied in v6.0 with the following interesting design, visible in the Open Source codebase and used in the default PyrrhoSvr build.

From v6.0 servers holding slave databases and partitions check their copy information is up-to-date only on start-up, and thereafter receive Push notifications about any changes to database length. They will retrieve the details of the changes when and if they need to. This mechanism works in a hierarchical way so that the Push load is shared by intermmediate servers if these have been configured. All this did complicate the implementation, since server-server communication channels need to be between threads, but it is worthwhile for theoretical reasons.

I will update the screenshots and documentation in the distributed and partitioned tutorials in the next days.

D: Enhancements to the HTTP/REST services

Previous posts in this blog have referred to ETags and RESTViews. A paper on these has now been published, thanks to Friz Laux, Mart Laiho and Carolyn Begg. The practical effect of these features could be adopted much more widely than Pyrrho, and I hope to return to this aspect soon.

Basically, it would be great if all DBMS provided a really simple REST service so that a simple GET would get a table (or other query results) in Json format together with an RFC7232 ETag. Even better if such a view was also potentially updatable with PUT, POST and DELETE. If this is done, database applications can always use WebRequests instead of the clunky APIs: JDBC,ODBC, ADO.NET, JPA.... The authorisation arrangements for this should also be simple and preferably role based, and use the If-Match HTTP header to check ETags.

This works already for Pyrrho (If-Match from v6), and there is more:

HTTP is stateless so the simple steps described above don't provide a way of making several changes in a single HTTP call. But at least for a single database, ACID transactions can be supported by a simple POST of an SQL statement to the database (+role) URL, since SQL statements can be compound and have exception handlers etc. And the POST can be guarded by If-Match to if the SQL statement contains data previously obtained from the database.

It is definitely a step too far in my opinion to try to use these mechanisms for transactions that change more than one database.

As usual, any comments welcome, preferably to malcolm.crowe at uws.ac.uk (make sure the subject line of the email is relevant).